Interaction restraints

Interaction restraints can be used to define interactions between entire subunits, domains or single residues.

They can be defined in JSON configuration file like this:

Interaction between two proteins:

{
    "type": "connectivity",
    "active": true,
    "name": "Ely5-Nup120_interaction1",
    "comment": "Ely5 - Nup120 interaction",
    "data": [
        [{"subunit": "Nup120", "serie": "NR_1", "copies": [0]}, {"subunit": "Ely5", "serie": "NR_1", "copies": [0]}]
    ],
    "weight": 0.1,
    "k": 1,
    "distance": 7.0,
    "first_copy_only": true,
    "repr_resolution": 10
}

Distance between specific residues:

{
    "type": "connectivity",
    "active": true,
    "name": "Nup107_connectivity",
    "comment": "Keep the N and C domains of Nup107 close to account for the three missing helices",
    "data": [
        [{"subunit": "Nup107", "serie": "NR_1", "resi_ranges": [494]}, {"subunit": "Nup107", "serie": "NR_1", "resi_ranges": [580]}],
        [{"subunit": "Nup107", "serie": "NR_2", "resi_ranges": [494]}, {"subunit": "Nup107", "serie": "NR_2", "resi_ranges": [580]}],
        [{"subunit": "Nup107", "serie": "NR_1", "resi_ranges": [512]}, {"subunit": "Nup107", "serie": "NR_1", "resi_ranges": [595]}],
        [{"subunit": "Nup107", "serie": "NR_2", "resi_ranges": [512]}, {"subunit": "Nup107", "serie": "NR_2", "resi_ranges": [595]}]
    ],
    "weight": 1000.0,
    "k": 1,
    "distance": 25.0,
    "first_copy_only": true,
    "repr_resolution": 1
}

Here, each pair of residues specified in the "data" list will be restrained to distance below 25A

Parameters

type: Must be “connectivity”
active: true or false, whether the restraint should be created, you can set to false to save on loading time if you don’t need this restraint (even if it’s true, you still need to add it to a scoring function to have it an effect)
name: whatever name. Use this name to refer to this restraint in Parameter file when defining the scoring functions
comment: Optional comment, useful for documenting
data: A list of pairs of Selectors between which the interaction restraints should be defined
weight: Weight of this restraint
first_copy_only: true or false, Apply only to the first molecule copy of each series?
repr_resolution: The resolution of representation to which this restraint should be applied
k: Spring constant for the harmonic potential, redundant to weight, ignore
distance: Distance threshold below which the restraint is satisfied. The score is 0 below this threshold and harmonic above.